I have the unmapped reads from a RNAseq experiement (unmapped.bam) and I want to try and map these to a different genome. I have sorted my unmapped.bam using

samtools view -n unmapped.bam unmappedsorted.bam

I have checked the files have the same number of reads. I then wanted to convert the unmappedsorted.bam to fastq format so that I may use tophat to map the 'unmappedsorted' to the other genome. I tried: